Organically modified clays have been reported as a promising class of adsorbents for the treatment of per- and polyfluoroalkyl substances (PFAS), a group of emerging contaminants of widespread concerns. Here, we reported the development and evaluation of ionic liquid (IL)-modified clays prepared with various natural clays to explore the role of clay substrate in the adsorption of eight persistent perfluoroalkyl acids (PFAAs). Based on detailed adsorption isotherm study, we found that the adsorption capacities of PFAAs were closely related to the cation exchange capacities of the raw clays and correspondingly the IL loadings of the modified clays. Additionally, a positive correlation was observed between the adsorption affinity of PFAAs onto IL-modified clays and the octanol–water distribution coefficient (Dow) of PFAAs. Adsorption free energy analysis suggested that both electrostatic and hydrophobic interactions played important roles in the adsorption of PFAAs onto IL-modified clays. Although electrostatic interactions were more predominant, the contribution of hydrophobic interactions increased with the increasing carbon number of perfluoroalkyl moiety of PFAAs, resulting in more favorable adsorption of long-chain PFAAs than their short-chain homologs. The performance of IL-modified clays was further demonstrated for the removal of PFAA mixtures under environmentally relevant conditions. Overall, results of this work can provide important insights into guiding the design of organically modified clay adsorbents for PFAS treatment.